Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 23580.58 
• Atom Count: 1956 
• Residue Count: 223 
• Unique protein chains: 1

5F6M

Isotropic Trypsin Model for Comparison of Diffuse Scattering

• DOI: 10.2210/pdb5F6M/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus


• Deposited: 2015-12-06 Released: 2016-01-06 
• Deposition Author(s): Van Benschoten, A.H., Wall, M.E., Fraser, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.154 
• R-Value Work: 0.145 

Literature

Measuring and modeling diffuse scattering in protein X-ray crystallography.

Van Benschoten, A.H., Liu, L., Gonzalez, A., Brewster, A.S., Sauter, N.K., Fraser, J.S., Wall, M.E.

(2016) Proc.Natl.Acad.Sci.USA 113: 4069-4074

• PubMed: 27035972 
• DOI: 10.1073/pnas.1524048113
• Primary Citation of Related Structures:  
  5F66


• PubMed Abstract: 
  

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.

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Organizational Affiliation: 

Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158;

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
BEN	A	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.154 
• R-Value Work: 0.145 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 
  10.15785/SBGRID/201 SBGrid

Unit Cell:

Length (Å)	Angle (°)
a = 54.810	α = 90.00
b = 58.510	β = 90.00
c = 67.420	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-06 
• Released Date: 2016-01-06 
• Deposition Author(s): Van Benschoten, A.H., Wall, M.E., Fraser, J.S.

Revision History 

• Version 1.0: 2016-01-06
  Type: Initial release
• Version 1.1: 2016-03-30
  Type: Database references
• Version 1.2: 2016-04-13
  Type: Database references
• Version 1.3: 2016-06-22
  Type: Database references